3 High Quality Graphics in R
## -----------------------------------------------------------------------------
## ## produces the xkcd-plotting image used below
library("xkcd")
## Loading required package: ggplot2
## Loading required package: extrafont
## Registering fonts with R
library("showtext")
## Loading required package: sysfonts
## Loading required package: showtextdb
##
## Attaching package: 'showtextdb'
## The following object is masked from 'package:extrafont':
##
## font_install
library("sysfonts")
library("tibble")
##
introplotdata = tibble(
y = c(seq(-8, 1, length=25)^2, rep(1, 5), seq(1, 5,length=25)^2)^2,
x = seq(1, 55, length.out = length(y)))
dataman = tibble(
x = 30,
y = 400,
scale = 100,
ratioxy = 0.1,
angleofspine = -pi/2 ,
anglerighthumerus = -pi/6,
anglelefthumerus = pi * 7/6,
anglerightradius = 0,
angleleftradius = 0,
angleleftleg = 19*pi/12,
anglerightleg = 17*pi/12,
angleofneck = 1.4*pi)
mapping = do.call(aes_string, colnames(dataman) %>% (function(x) setNames(as.list(x), x)))
## Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
## ℹ Please use tidy evaluation idioms with `aes()`.
## ℹ See also `vignette("ggplot2-in-packages")` for more information.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
ggplot(introplotdata) + geom_line(aes(x = x, y = y), size = 2) +
xkcdaxis(c(0, 50), c(0, 1000)) + xlab("Time to make plot in minutes") +
ylab("Time to understand plot in minutes") + xkcdman(mapping, dataman) +
theme(axis.title.x = element_text(margin = margin(15, 0, 0, 0)))
## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## Warning in theme_xkcd(): Not xkcd fonts installed! See vignette("xkcd-intro")
## -----------------------------------------------------------------------------
head(DNase)
## Run conc density
## 1 1 0.04882812 0.017
## 2 1 0.04882812 0.018
## 3 1 0.19531250 0.121
## 4 1 0.19531250 0.124
## 5 1 0.39062500 0.206
## 6 1 0.39062500 0.215
plot(DNase$conc, DNase$density)
## -----------------------------------------------------------------------------
plot(DNase$conc, DNase$density,
ylab = attr(DNase, "labels")$y,
xlab = paste(attr(DNase, "labels")$x, attr(DNase, "units")$x),
pch = 3,
col = "blue")
## -----------------------------------------------------------------------------
hist(DNase$density, breaks=25, main = "")
boxplot(density ~ Run, data = DNase)
## -----------------------------------------------------------------------------
library("Hiiragi2013")
## Loading required package: affy
## Loading required package: BiocGenerics
##
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, basename, cbind, colnames,
## dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
## grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
## order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
## rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
## union, unique, unsplit, which.max, which.min
## Loading required package: Biobase
## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
## Loading required package: boot
## Loading required package: clue
## Loading required package: cluster
## Loading required package: genefilter
## Loading required package: geneplotter
## Loading required package: lattice
##
## Attaching package: 'lattice'
## The following object is masked from 'package:boot':
##
## melanoma
## Loading required package: annotate
## Loading required package: AnnotationDbi
## Loading required package: stats4
## Loading required package: IRanges
## Loading required package: S4Vectors
##
## Attaching package: 'S4Vectors'
## The following objects are masked from 'package:base':
##
## expand.grid, I, unname
##
## Attaching package: 'IRanges'
## The following object is masked from 'package:grDevices':
##
## windows
## Loading required package: XML
## Loading required package: gplots
##
## Attaching package: 'gplots'
## The following object is masked from 'package:IRanges':
##
## space
## The following object is masked from 'package:S4Vectors':
##
## space
## The following object is masked from 'package:stats':
##
## lowess
## Loading required package: gtools
##
## Attaching package: 'gtools'
## The following objects are masked from 'package:boot':
##
## inv.logit, logit
## Loading required package: KEGGREST
## Loading required package: MASS
##
## Attaching package: 'MASS'
## The following object is masked from 'package:AnnotationDbi':
##
## select
## The following object is masked from 'package:genefilter':
##
## area
## Loading required package: mouse4302.db
## Loading required package: org.Mm.eg.db
##
##
## Loading required package: RColorBrewer
## Loading required package: xtable
data("x")
dim(Biobase::exprs(x))
## [1] 45101 101
## -----------------------------------------------------------------------------
head(pData(x), n = 2)
## File.name Embryonic.day Total.number.of.cells lineage genotype
## 1 E3.25 1_C32_IN E3.25 32 WT
## 2 E3.25 2_C32_IN E3.25 32 WT
## ScanDate sampleGroup sampleColour
## 1 E3.25 2011-03-16 E3.25 #CAB2D6
## 2 E3.25 2011-03-16 E3.25 #CAB2D6
## -----------------------------------------------------------------------------
library("dplyr")
##
## Attaching package: 'dplyr'
## The following object is masked from 'package:MASS':
##
## select
## The following object is masked from 'package:AnnotationDbi':
##
## select
## The following objects are masked from 'package:IRanges':
##
## collapse, desc, intersect, setdiff, slice, union
## The following objects are masked from 'package:S4Vectors':
##
## first, intersect, rename, setdiff, setequal, union
## The following object is masked from 'package:Biobase':
##
## combine
## The following objects are masked from 'package:BiocGenerics':
##
## combine, intersect, setdiff, union
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
groups = group_by(pData(x), sampleGroup) %>%
summarise(n = n(), color = unique(sampleColour))
groups
## # A tibble: 8 × 3
## sampleGroup n color
## <chr> <int> <chr>
## 1 E3.25 36 #CAB2D6
## 2 E3.25 (FGF4-KO) 17 #FDBF6F
## 3 E3.5 (EPI) 11 #A6CEE3
## 4 E3.5 (FGF4-KO) 8 #FF7F00
## 5 E3.5 (PE) 11 #B2DF8A
## 6 E4.5 (EPI) 4 #1F78B4
## 7 E4.5 (FGF4-KO) 10 #E31A1C
## 8 E4.5 (PE) 4 #33A02C
## -----------------------------------------------------------------------------
## f(x) %>% g(y) %>% h
## h(g(f(x), y))
## -----------------------------------------------------------------------------
library("ggplot2")
ggplot(DNase, aes(x = conc, y = density)) + geom_point()
## -----------------------------------------------------------------------------
ggplot(groups, aes(x = sampleGroup, y = n)) +
geom_bar(stat = "identity")
## -----------------------------------------------------------------------------
## check an assertion made in the text above
stopifnot(formals(ggplot2::geom_bar)$stat=="count")
## -----------------------------------------------------------------------------
groupColor = setNames(groups$color, groups$sampleGroup)
## -----------------------------------------------------------------------------
ggplot(groups, aes(x = sampleGroup, y = n, fill = sampleGroup)) +
geom_bar(stat = "identity") +
scale_fill_manual(values = groupColor, name = "Groups") +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
## -----------------------------------------------------------------------------
gg = ggplot(DNase, aes(x = conc, y = density)) + geom_point()
## -----------------------------------------------------------------------------
## gg
print(gg)
## -----------------------------------------------------------------------------
ggplot2::ggsave("DNAse-histogram-demo.pdf", plot = gg)
## Saving 7 x 5 in image
## -----------------------------------------------------------------------------
file.remove("DNAse-histogram-demo.pdf")
## [1] TRUE
## -----------------------------------------------------------------------------
library("mouse4302.db")
## -----------------------------------------------------------------------------
## # I used this code to find the below two probes
idx = order(rowVars(Biobase::exprs(x)), decreasing=TRUE)[seq_len(2000)]
cc = cor(t(Biobase::exprs(x)[idx,]))
cco = order(cc)[seq(1, 1001, by=2) ]
jj2 = rownames(Biobase::exprs(x))[ idx[ (cco-1) %/% length(idx) + 1 ] ]
jj1 = rownames(Biobase::exprs(x))[ idx[ (cco-1) %% length(idx) + 1 ] ]
dftx = as.data.frame(t(Biobase::exprs(x)))
#par(ask=TRUE)
for(i in seq(along = cco)) {
df = AnnotationDbi::select(mouse4302.db,
keys = c(jj1[i], jj2[i]), keytype = "PROBEID",
columns = c("SYMBOL", "GENENAME"))
print(ggplot(dftx, aes( x = get(jj1[i]), y = get(jj2[i]))) +
geom_point(shape = 1) +
xlab(paste(jj1[i], df$SYMBOL[1])) +
ylab(paste(jj2[i], df$SYMBOL[2])) +
ggtitle(round(cc[jj1[i], jj2[i]], 3)) + geom_smooth(method = "loess"))
}
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:many mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## 'select()' returned 1:1 mapping between keys and columns
## `geom_smooth()` using formula = 'y ~ x'
## -----------------------------------------------------------------------------
dftx = data.frame(t(Biobase::exprs(x)), pData(x))
ggplot( dftx, aes( x = X1426642_at, y = X1418765_at )) +
geom_point( shape = 1 ) +
geom_smooth( method = "loess" )
## `geom_smooth()` using formula = 'y ~ x'
## -----------------------------------------------------------------------------
stopifnot(is(dftx, "data.frame"))
## -----------------------------------------------------------------------------
.one <- AnnotationDbi::select(mouse4302.db,
keys = "1418765_at",
keytype = "PROBEID",
columns = "SYMBOL")$SYMBOL
## 'select()' returned 1:1 mapping between keys and columns
.two <- AnnotationDbi::select(mouse4302.db,
keys = "1426642_at",
keytype = "PROBEID",
columns = "SYMBOL")$SYMBOL
## 'select()' returned 1:1 mapping between keys and columns
## -----------------------------------------------------------------------------
ggplot( dftx, aes( x = X1426642_at, y = X1418765_at )) +
geom_point( aes( color = sampleColour), shape = 19 ) +
geom_smooth( method = "loess" ) +
scale_color_discrete( guide = "none" )
## `geom_smooth()` using formula = 'y ~ x'
## -----------------------------------------------------------------------------
library("mouse4302.db")
## -----------------------------------------------------------------------------
AnnotationDbi::select(mouse4302.db,
keys = c("1426642_at", "1418765_at"), keytype = "PROBEID",
columns = c("SYMBOL", "GENENAME"))
## 'select()' returned 1:1 mapping between keys and columns
## PROBEID SYMBOL GENENAME
## 1 1426642_at Fn1 fibronectin 1
## 2 1418765_at Timd2 T cell immunoglobulin and mucin domain containing 2
## -----------------------------------------------------------------------------
dfx = as.data.frame(Biobase::exprs(x))
ggplot(dfx, aes(x = `20 E3.25`)) + geom_histogram(binwidth = 0.2)
## -----------------------------------------------------------------------------
pb = ggplot(groups, aes(x = sampleGroup, y = n))
## -----------------------------------------------------------------------------
class(pb)
## [1] "gg" "ggplot"
pb
## -----------------------------------------------------------------------------
pb = pb + geom_bar(stat = "identity")
pb = pb + aes(fill = sampleGroup)
pb = pb + theme(axis.text.x = element_text(angle = 90, hjust = 1))
pb = pb + scale_fill_manual(values = groupColor, name = "Groups")
pb
## -----------------------------------------------------------------------------
pb.polar = pb + coord_polar() +
theme(axis.text.x = element_text(angle = 0, hjust = 1),
axis.text.y = element_blank(),
axis.ticks = element_blank()) +
xlab("") + ylab("")
pb.polar
## -----------------------------------------------------------------------------
selectedProbes = c( Fgf4 = "1420085_at", Gata4 = "1418863_at",
Gata6 = "1425463_at", Sox2 = "1416967_at")
## -----------------------------------------------------------------------------
## # How I found the selectedProbes:
## AnnotationDbi::select(mouse4302.db,
## keys = c("Fgf4", "Sox2", "Gata6", "Gata4"), keytype = "SYMBOL",
## columns = c("PROBEID"))
## -----------------------------------------------------------------------------
selectedProbes2 = AnnotationDbi::select(mouse4302.db,
keys = selectedProbes, keytype = "PROBEID", columns = c("SYMBOL"))
## 'select()' returned 1:1 mapping between keys and columns
stopifnot(identical(sort(selectedProbes2$SYMBOL), sort(names(selectedProbes))),
all(selectedProbes[selectedProbes2$SYMBOL] == selectedProbes2$PROBEID))
## -----------------------------------------------------------------------------
library("reshape2")
genes = melt(Biobase::exprs(x)[selectedProbes, ],
varnames = c("probe", "sample"))
## -----------------------------------------------------------------------------
genes$gene =
names(selectedProbes)[match(genes$probe, selectedProbes)]
head(genes)
## probe sample value gene
## 1 1420085_at 1 E3.25 3.027715 Fgf4
## 2 1418863_at 1 E3.25 4.843137 Gata4
## 3 1425463_at 1 E3.25 5.500618 Gata6
## 4 1416967_at 1 E3.25 1.731217 Sox2
## 5 1420085_at 2 E3.25 9.293016 Fgf4
## 6 1418863_at 2 E3.25 5.530016 Gata4
## -----------------------------------------------------------------------------
ggplot(genes, aes(x = gene, y = value)) +
stat_summary(fun = mean, geom = "bar")
## -----------------------------------------------------------------------------
library("Hmisc")
## Loading required package: survival
##
## Attaching package: 'survival'
## The following object is masked from 'package:boot':
##
## aml
## Loading required package: Formula
##
## Attaching package: 'Hmisc'
## The following objects are masked from 'package:dplyr':
##
## src, summarize
## The following objects are masked from 'package:xtable':
##
## label, label<-
## The following object is masked from 'package:AnnotationDbi':
##
## contents
## The following object is masked from 'package:Biobase':
##
## contents
## The following objects are masked from 'package:base':
##
## format.pval, units
ggplot(genes, aes( x = gene, y = value, fill = gene)) +
stat_summary(fun = mean, geom = "bar") +
stat_summary(fun.data = mean_cl_normal, geom = "errorbar",
width = 0.25)
## -----------------------------------------------------------------------------
p = ggplot(genes, aes( x = gene, y = value, fill = gene))
p + geom_boxplot()
## -----------------------------------------------------------------------------
p + geom_dotplot(binaxis = "y", binwidth = 1/6,
stackdir = "center", stackratio = 0.75,
aes(color = gene))
library("ggbeeswarm")
p + geom_beeswarm(aes(color = gene))
## ------------
#-----------------------------------------------------------------
ggplot(genes, aes( x = value, color = gene)) + geom_density()
## -----------------------------------------------------------------------------
p + geom_violin()
## -----------------------------------------------------------------------------
library("ggridges")
ggplot(genes, aes(x = value, y = gene, fill = gene)) +
geom_density_ridges()
## Picking joint bandwidth of 0.729
## -----------------------------------------------------------------------------
top42 = order(rowMeans(Biobase::exprs(x)), decreasing = TRUE)[1:42]
g42 = melt(Biobase::exprs(x)[rev(top42), ], varnames = c("probe", "sample"))
ggplot(g42, aes(x = value, y = probe))
## -----------------------------------------------------------------------------
ggplot(g42, aes(x = value, y = probe)) +
geom_density_ridges() + theme(legend.position = "none",
axis.title.y = element_blank(), axis.text.y = element_blank(),
axis.ticks.y = element_blank()) + xlim(13, 15)
## Picking joint bandwidth of 0.0683
## Warning: Removed 35 rows containing non-finite values (`stat_density_ridges()`).
## -----------------------------------------------------------------------------
simdata = rnorm(70)
tibble(index = seq(along = simdata),
sx = sort(simdata)) %>%
ggplot(aes(x = sx, y = index)) + geom_step()
## -----------------------------------------------------------------------------
ggplot(genes, aes( x = value, color = gene)) + stat_ecdf()
## -----------------------------------------------------------------------------
## # I used the functon bimodality_coefficient from the modes package to identify the most
## # bimodal looking array, number 64
## j0 = which.max(vapply(seq_len(ncol(x)), function(j){
## modes :: bimodality_coefficient(Biobase::exprs(x)[, j])
## }, numeric(1)))
## -----------------------------------------------------------------------------
ggplot(dfx, aes(x = `64 E4.5 (EPI)`)) + geom_histogram(bins = 100)
ggplot(dfx, aes(x = 2 ^ `64 E4.5 (EPI)`)) +
geom_histogram(binwidth = 20) + xlim(0, 1500)
## Warning: Removed 1457 rows containing non-finite values (`stat_bin()`).
## Warning: Removed 2 rows containing missing values (`geom_bar()`).
## -----------------------------------------------------------------------------
scp = ggplot(dfx, aes(x = `59 E4.5 (PE)` ,
y = `92 E4.5 (FGF4-KO)`))
scp + geom_point()
## -----------------------------------------------------------------------------
scp + geom_point(alpha = 0.1)
## -----------------------------------------------------------------------------
scp + geom_density2d()
## -----------------------------------------------------------------------------
scp + geom_density2d(h = 0.5, bins = 60)
library("RColorBrewer")
colorscale = scale_fill_gradientn(
colors = rev(brewer.pal(9, "YlGnBu")),
values = c(0, exp(seq(-5, 0, length.out = 100))))
scp + stat_density2d(h = 0.5, bins = 60,
aes( fill = after_stat(level)), geom = "polygon") +
colorscale + coord_fixed()
## -----------------------------------------------------------------------------
scp + geom_hex() + coord_fixed()
scp + geom_hex(binwidth = c(0.2, 0.2)) + colorscale +
coord_fixed()
## -----------------------------------------------------------------------------
library("ggthemes")
sunsp = tibble(year = time(sunspot.year),
number = as.numeric(sunspot.year))
sp = ggplot(sunsp, aes(x = year, y = number)) + geom_line()
sp
## Don't know how to automatically pick scale for object of type <ts>. Defaulting
## to continuous.
ratio = with(sunsp, bank_slopes(year, number))
sp + coord_fixed(ratio = ratio)
## Don't know how to automatically pick scale for object of type <ts>. Defaulting
## to continuous.
## -----------------------------------------------------------------------------
library("magrittr")
dftx$lineage %<>% sub("^$", "no", .)
dftx$lineage %<>% factor(levels = c("no", "EPI", "PE", "FGF4-KO"))
ggplot(dftx, aes(x = X1426642_at, y = X1418765_at)) +
geom_point() + facet_grid( . ~ lineage )
## -----------------------------------------------------------------------------
ggplot(dftx,
aes(x = X1426642_at, y = X1418765_at)) + geom_point() +
facet_grid( Embryonic.day ~ lineage )
## -----------------------------------------------------------------------------
ggplot(mutate(dftx, Tdgf1 = cut(X1450989_at, breaks = 4)),
aes(x = X1426642_at, y = X1418765_at)) + geom_point() +
facet_wrap( ~ Tdgf1, ncol = 2 )
## -----------------------------------------------------------------------------
library("plotly")
##
## Attaching package: 'plotly'
## The following object is masked from 'package:Hmisc':
##
## subplot
## The following object is masked from 'package:MASS':
##
## select
## The following object is masked from 'package:AnnotationDbi':
##
## select
## The following object is masked from 'package:IRanges':
##
## slice
## The following object is masked from 'package:S4Vectors':
##
## rename
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
plot_ly(economics, x = ~ date, y = ~ unemploy / pop)
## No trace type specified:
## Based on info supplied, a 'scatter' trace seems appropriate.
## Read more about this trace type -> https://plotly.com/r/reference/#scatter
## No scatter mode specifed:
## Setting the mode to markers
## Read more about this attribute -> https://plotly.com/r/reference/#scatter-mode
## -----------------------------------------------------------------------------
data("volcano")
volcanoData = list(
x = 10 * seq_len(nrow(volcano)),
y = 10 * seq_len(ncol(volcano)),
z = volcano,
col = terrain.colors(500)[cut(volcano, breaks = 500)]
)
library("rgl")
with(volcanoData, persp3d(x, y, z, color = col))
## -----------------------------------------------------------------------------
.volcanocut = cut(volcano, breaks = 500)
stopifnot(!any(is.na(.volcanocut)), all(as.integer(.volcanocut) %in% 1:500))
## -----------------------------------------------------------------------------
par(mai = rep(0, 4)) # A numerical vector of the form c(bottom, left, top, right) which gives the margin size specified in inches.
pie(rep(1, 8), col=1:8)
tibble(u = factor(1:8), v = 1)
## # A tibble: 8 × 2
## u v
## <fct> <dbl>
## 1 1 1
## 2 2 1
## 3 3 1
## 4 4 1
## 5 5 1
## 6 6 1
## 7 7 1
## 8 8 1
## -----------------------------------------------------------------------------
ggplot(tibble(u = factor(1:8), v = 1),
aes(x = "", y = v, fill = u)) +
geom_bar(stat = "identity", width = 1) +
coord_polar("y", start = 0) + theme_void()
## -----------------------------------------------------------------------------
par(mai = c(0, 0.8, 0, 0))
display.brewer.all()
## -----------------------------------------------------------------------------
head(brewer.pal.info)
## maxcolors category colorblind
## BrBG 11 div TRUE
## PiYG 11 div TRUE
## PRGn 11 div TRUE
## PuOr 11 div TRUE
## RdBu 11 div TRUE
## RdGy 11 div FALSE
table(brewer.pal.info$category)
##
## div qual seq
## 9 8 18
## -----------------------------------------------------------------------------
brewer.pal(4, "RdYlGn") #Creates nice looking color palettes especially for thematic maps
## [1] "#D7191C" "#FDAE61" "#A6D96A" "#1A9641"
## -----------------------------------------------------------------------------
par(mai = rep(0.1, 4))
mypalette = colorRampPalette(
c("darkorange3", "white","darkblue")
)(100)
head(mypalette)
## [1] "#CD6600" "#CE6905" "#CF6C0A" "#D06F0F" "#D17214" "#D27519"
image(matrix(1:100, nrow = 100, ncol = 10), col = mypalette,
xaxt = "n", yaxt = "n", useRaster = TRUE)
## -----------------------------------------------------------------------------
library("pheatmap")
topGenes = order(rowVars(Biobase::exprs(x)), decreasing = TRUE)[1:500]
rowCenter = function(x) { x - rowMeans(x) }
pheatmap( rowCenter(Biobase::exprs(x)[ topGenes, ] ),
show_rownames = FALSE, show_colnames = FALSE,
breaks = seq(-5, +5, length = 101),
annotation_col =
pData(x)[, c("sampleGroup", "Embryonic.day", "ScanDate") ],
annotation_colors = list(
sampleGroup = groupColor,
genotype = c(`FGF4-KO` = "chocolate1", `WT` = "azure2"),
Embryonic.day = setNames(brewer.pal(9, "Blues")[c(3, 6, 9)],
c("E3.25", "E3.5", "E4.5")),
ScanDate = setNames(brewer.pal(nlevels(x$ScanDate), "YlGn"),
levels(x$ScanDate))
),
cutree_rows = 4
)
## -----------------------------------------------------------------------------
groupColor[1]
## E3.25
## "#CAB2D6"
## -----------------------------------------------------------------------------
hexvals = sapply(1:3, function(i) substr(groupColor[1], i*2, i*2+1))
decvals = strtoi(paste0("0x", hexvals))
## -----------------------------------------------------------------------------
library("colorspace")
library("grid")
plothcl = function(h, c, l, what, x0 = 0.5, y0 = 0.5, default.units = "npc", ...) {
switch(what,
"c" = {
stopifnot(length(l)==1)
n = length(c)
},
"l" = {
stopifnot(length(c)==1)
n = length(l)
},
stop("Sapperlot"))
cr = seq(0.1, 0.5, length = n+1)
dr = 0.05 / n
for (j in seq_len(n)) {
r = c(cr[j]+dr, cr[j+1]-dr)
for(i in 1:(length(h)-1)){
phi = seq(h[i], h[i+1], by=1)/180*pi
px = x0 + c(r[1]*cos(phi), r[2]*rev(cos(phi)))
py = y0 + c(r[1]*sin(phi), r[2]*rev(sin(phi)))
mycol = switch(what,
"c" = hcl(h=mean(h[i+(0:1)]), c=c[j], l=l),
"l" = hcl(h=mean(h[i+(0:1)]), c=c, l=l[j]))
grid::grid.polygon(px, py,
gp=gpar(col=mycol, fill=mycol),
default.units=default.units,...)
}
}
}
## -----------------------------------------------------------------------------
plothcl( h = seq(0, 360, by=3), c = seq(5, 75, by=10), l = 75, what="c")
grid.newpage()
plothcl( h = seq(0, 360, by=3), c = 55, l = seq(20, 100, by=10), what="l")
## -----------------------------------------------------------------------------
gg = ggplot(tibble(A = Biobase::exprs(x)[, 1], M = rnorm(length(A))),
aes(y = M))
gg + geom_point(aes(x = A), size = 0.2)
gg + geom_point(aes(x = rank(A)), size = 0.2)
## -----------------------------------------------------------------------------
volume = function(rho, nu)
pi^(nu/2) * rho^nu / gamma(nu/2+1)
ggplot(tibble(nu = 1:15,
Omega = volume(1, nu)), aes(x = nu, y = Omega)) +
geom_line() +
xlab(expression(nu)) + ylab(expression(Omega)) +
geom_text(label =
"Omega(rho,nu)==frac(pi^frac(nu,2)~rho^nu, Gamma(frac(nu,2)+1))",
parse = TRUE, x = 6, y = 1.5)
## -----------------------------------------------------------------------------
ggplot(genes, aes( x = value, color = gene)) + stat_ecdf() +
theme(text = element_text(family = "serif"))
## -----------------------------------------------------------------------------
ggplot(genes, aes( x = value, color = gene)) + stat_ecdf() + theme(text = element_text(family = "Bauhaus 93"))
## -----------------------------------------------------------------------------
library("ggbio")
## Registered S3 method overwritten by 'GGally':
## method from
## +.gg ggplot2
## Need specific help about ggbio? try mailing
## the maintainer or visit https://lawremi.github.io/ggbio/
##
## Attaching package: 'ggbio'
## The following object is masked from 'package:Hmisc':
##
## zoom
## The following objects are masked from 'package:ggplot2':
##
## geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
## xlim
data("hg19IdeogramCyto", package = "biovizBase")
plotIdeogram(hg19IdeogramCyto, subchr = "chr1")
## Found more than one class "simpleUnit" in cache; using the first, from namespace 'hexbin'
## Also defined by 'ggbio'
## -----------------------------------------------------------------------------
library("GenomicRanges")
## Loading required package: GenomeInfoDb
data("darned_hg19_subset500", package = "biovizBase")
autoplot(darned_hg19_subset500, layout = "karyogram",
aes(color = exReg, fill = exReg))
## Warning in getIdeoGR(data): geom(ideogram) need valid seqlengths information for accurate mapping,
## now use reduced information as ideogram...
## Warning in getIdeoGR(data): geom(ideogram) need valid seqlengths information for accurate mapping,
## now use reduced information as ideogram...
## Scale for x is already present.
## Adding another scale for x, which will replace the existing scale.
## Scale for x is already present.
## Adding another scale for x, which will replace the existing scale.
## -----------------------------------------------------------------------------
data("ideoCyto", package = "biovizBase")
dn = darned_hg19_subset500
seqlengths(dn) = seqlengths(ideoCyto$hg19)[names(seqlengths(dn))]
dn = keepSeqlevels(dn, paste0("chr", c(1:22, "X")))
autoplot(dn, layout = "karyogram", aes(color = exReg, fill = exReg))
## Scale for x is already present.
## Adding another scale for x, which will replace the existing scale.
## Scale for x is already present.
## Adding another scale for x, which will replace the existing scale.
## -----------------------------------------------------------------------------
darned_hg19_subset500[1:2,]
## GRanges object with 2 ranges and 10 metadata columns:
## seqnames ranges strand | inchr inrna snp
## <Rle> <IRanges> <Rle> | <character> <character> <character>
## [1] chr5 86618225 - | A I <NA>
## [2] chr7 99792382 - | A I <NA>
## gene seqReg exReg source ests esta
## <character> <character> <character> <character> <integer> <integer>
## [1] <NA> O <NA> amygdala 0 0
## [2] <NA> O <NA> <NA> 0 0
## author
## <character>
## [1] 15342557
## [2] 15342557
## -------
## seqinfo: 23 sequences from an unspecified genome; no seqlengths
## -----------------------------------------------------------------------------
stopifnot(is(darned_hg19_subset500, "GRanges"), identical(start(darned_hg19_subset500),end(darned_hg19_subset500)))
## -----------------------------------------------------------------------------
ggcars = ggplot(mtcars, aes(x = hp, y = mpg)) + geom_point(size = 5, color = 'red')
ggcars
ggcars + theme_bw()
ggcars + theme_minimal()
